#include "sequence.hpp"
#include "listvector.hpp"
+
//**********************************************************************************************************************
-vector<string> ListSeqsCommand::getValidParameters(){
+vector<string> ListSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ListSeqsCommand", "getValidParameters");
+ m->errorOut(e, "ListSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ListSeqsCommand::ListSeqsCommand(){
+string ListSeqsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["accnos"] = tempOutNames;
+ string helpString = "";
+ helpString += "The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+ helpString += "The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport. You must provide one of these parameters.\n";
+ helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
+ helpString += "Example list.seqs(fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ListSeqsCommand", "getRequiredParameters");
+ m->errorOut(e, "ListSeqsCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredFiles(){
+ListSeqsCommand::ListSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ListSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
exit(1);
}
}
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
}
//**********************************************************************************************************************
-void ListSeqsCommand::help(){
- try {
- m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n");
- m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport. You must provide one of these parameters.\n");
- m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
- m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ListSeqsCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int ListSeqsCommand::execute(){
try {
ofstream out;
m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
//output to .accnos file
for (int i = 0; i < names.size(); i++) {
out.close();
if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
-
+
+ m->setAccnosFile(outputFileName);
+
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
+ //set accnos file as new current accnosfile
+ string current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
return 0;
}